(OpenGL 3.1 - 4.2) Dynamic Uniform Arrays?

Lets say I have 2 species such as humans and ponies. They have different skeletal systems so the uniform bone array will have to be different for each species. Do I have to implement two separate shader programs able to render each bone array properly or is there a way to dynamically declare uniform arrays and iterate through that dynamic array instead?

Keeping in mind performance (There's all of the shaders suck at decision branching going around).